UEF commander drones

I am new and have twice came across UEF players who rush commander drones then procced to capture my mexes and build bases behind my lines, while the enemy commander is accross the map, is this a mechanic or exploit ?

This is allowed. Those drones should be very easy to kill with fighters. Aa works also. Suggest you try to counter those with fighter planes.

the drones can be shot down with Mobile anti-air or tech 1 interceptors

"The needs of the many outweigh the needs of the few" - Spock

The solution is (1) scouting, if you send out scout planes you should find the drones and (2) make interceptors to shoot them down

Scouting means looking at the enemy ACU to find out if he's got a backpack, and flying around the map to find the drones so your interceptors can kill them.

You can tell if there's a drone by scouting the enemy ACU with a scout plane. While the ACU is upgrading, you can see the "glow." A drone upgrade will be on the back. A T2, gun upgrade, or nano repair will be on one of the arms. (While it is upgrading, you can look to see whether the "glow" is on the ACU's back, or on one of the arms. You might need to zoom in to tell the difference, but it's worth knowing.) The other backpack upgrades are too expensive for the early game (for TML or shield, you basically need a T2 pgen, for a teleporter you need T3 pgens). When the drone upgrade is finished, the ACU will be wearing a backpack. Once you know drones are out, you can make an effort to shoot them down.

If the enemy is investing in drones, and you're investing in an air factory to make interceptors, you should be ahead. You have an extra factory compared to the cost of making a drone. He was counting on using the drones to expand, but you shot them down, so he will have to start making engineers instead of tanks. With more tanks + air superiority you should be able to raid his stuff with tanks and make a bomber plane to pick off the expanding engies. If you just focus on the fundamentals and on being aggressive, you will be in a great spot to win against someone who makes an early drone.

Thanks for the info , have been doing so, but couldn'f find anything for against this mechanic being allowed

Not only is it allowed but that's exactly what the upgrade is for